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A framework for supervisory cooperative estimation in multi-agent linear time-invariant (LTI) systems is presented in the companion work (Part I). We introduced a set of sub-observers such that each estimates some states with a given set of input, output, and state information. A discerete-event system (DES) supervisory control framework is used for cooperation among the sub-observers. The supervisor selects a set of sub-observers to successfully estimate all states of the multi-agent system. In addition, in presence of a fault in the system, the supervisor reconfigures the set of selected sub-observers to minimize the fault impact on the estimation performance. Our general framework can be applied to any multi-agent system including industrial processes. In the companion paper (Part I), our proposed framework for the supervisory estimation is developed based on the notion of subobservers and DES supervisory control. In this paper (Part II), a DES-based combinatorial optimization method for selection of an optimal set of sub-observers is presented, the feasibility of the overall integrated sub-observers is validated, and the application of our proposed method in a practical industrial process is demonstrated through numerical simulations.